GapMind for catabolism of small carbon sources

 

Alignments for a candidate for bmpA in Rhodobacter ovatus JA234

Align Basic membrane lipoprotein, component of General nucleoside uptake porter, NupABC/BmpA (transports all common nucleosides as well as 5-fluorocytidine, inosine, deoxyuridine and xanthosine) (Martinussen et al., 2010) (Most similar to 3.A.1.2.12). NupA is 506aas with two ABC (C) domains. NupB has 8 predicted TMSs, NupC has 9 or 10 predicted TMSs in a 4 + 1 (or 2) + 4 arrangement (characterized)
to candidate WP_097028706.1 CRO07_RS00330 BMP family ABC transporter substrate-binding protein

Query= TCDB::D2BKA1
         (350 letters)



>NCBI__GCF_900207575.1:WP_097028706.1
          Length = 331

 Score =  147 bits (371), Expect = 4e-40
 Identities = 109/341 (31%), Positives = 160/341 (46%), Gaps = 36/341 (10%)

Query: 16  VAVLAGCRSHDAAGSGKAKTDLKAAIVTDTGGVNDRSFNQSAWEGLQSWGKENNLKKGTG 75
           +  LAG  +  A  +  A  D   A++ D GG  D+SFN++A+ G Q W +E     G  
Sbjct: 4   IRTLAGSAAAFALSAAGALAD--PALIFDLGGKFDKSFNEAAYNGAQRWVQET----GGS 57

Query: 76  YTYFQSNSASDYTTNYNSAEQQGYKLLFGIGFSLQDATSAAAKNNPKSNFVIVDSVIKDQ 135
           Y   +  S +          + G   +   GF+  D  +  A + P + F I+D+V+ +Q
Sbjct: 58  YKELEMQSEAQREQALRRLAETGANPIVMTGFAFGDVLNEVAPDYPDTRFAIIDAVV-EQ 116

Query: 136 KNVASATFADNESAYLAGVAAAKATKTNKIGFIGGMQSDVITRFEKGYEAGAKSVNPDIK 195
            NV S  F++++ +YL G+ AA A+K+  +GF+GGM   +I +F  GY  G K+V PD  
Sbjct: 117 PNVRSVIFSEHQGSYLVGMMAAMASKSGTVGFVGGMDIPLIRKFACGYAQGVKAVKPDAT 176

Query: 196 VDVQYAG----SFSDAAKGKTIAAAMYGAGDDVVYQCAGGVGTGVFSEAKALNSTKNEAD 251
           V +   G    +++D  KG  +A +    G DV+Y  AG  G GV   A   N       
Sbjct: 177 VVINMTGTTPAAWADPVKGAELARSQISQGADVIYAAAGSTGLGVLQAAADEN------- 229

Query: 252 KVWVIGVDQDQEYLGKYKSKDGKDSNFVLVSTIKEVGNVVKDIADKTKDGKFPGGTIVTY 311
            +  IGVD +Q +L   K         VL S IK V   V D            GT++  
Sbjct: 230 -ILSIGVDSNQNHLHPGK---------VLTSMIKRVDIAVHDAF--AAGAAIETGTVLA- 276

Query: 312 DLKNGGVNLGLDSAN-----SEIKDAVAKAKADIIDGKITV 347
           DLK  GV   LD  N     +E+K AV +A A I  G+  V
Sbjct: 277 DLKGDGVGYALDEHNAALVTAEMKAAVDEAAARIKSGETPV 317


Lambda     K      H
   0.310    0.128    0.353 

Gapped
Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 1
Number of Hits to DB: 291
Number of extensions: 16
Number of successful extensions: 4
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 1
Number of HSP's successfully gapped: 1
Length of query: 350
Length of database: 331
Length adjustment: 28
Effective length of query: 322
Effective length of database: 303
Effective search space:    97566
Effective search space used:    97566
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.8 bits)
S2: 49 (23.5 bits)

This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.

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About GapMind

Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.

A candidate for a step is "high confidence" if either:

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

Otherwise, a candidate is "medium confidence" if either:

Other blast hits with at least 50% coverage are "low confidence."

Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:

GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).

For more information, see:

If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know

by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory